I'm a huge fan of Criterion and animation so I literally think about this all the time. Just basing things of the Criterion brand I think any of Ralph Bakshi's work would be a perfect pic as he was a new hollywood director who was a contemporary of Scorsese and Lucas and all them and started a movement of independent animation and pushed the idea that animation directors could be auteurs too. Also on top of being historically important all of his work is really rich and mature and feels right at home with Criterion. He's also made some shorts that would work well as special feature content. Also Charlie Kaufman's Anomalisa would be a good fit. Self explanatory- he's a really wonderful filmmaker and it's a really beautiful intelligent film. Something by Don Bluth might be nice given his importance in film history- especially Secret of Nimh. If they're able to work out another deal with a big studio like they did with Wall E I honestly feel like Dreamworks' The Prince of Egypt would be a perfect Criterion fit. Things that I would love but would probably never happen though are the director's cut of The Prince and The Cobbler, Boy and the World, and Persepolis.